We're using Liferay 6.2 and getting a lot of error messages when creating a site based on a Site Template.
To reproduce:

1. Add JavaMelody Liferay plugin
2. Add SQL Monitoring (to mysql database) as explained on https://github.com/javamelody/javamelody/wiki/LiferayPlugin
3. In the Control Panel go to Sites
4. Add Site - Community Site
5. See the logs - note, we're not using staging.

ERRORcom.liferay.portal.service.persistence.impl.BasePersistenceImpl.processException(BasePersistenceImpl.java:244) [null][ajp-apr-8009-exec-456]
Caught unexpected exception java.lang.NullPointerException
2017-10-23 15:24:33 ERRORcom.liferay.portlet.sites.util.SitesImpl.mergeLayoutSetPrototypeLayouts(SitesImpl.java:1322) [null][ajp-apr-8009-exec-456]
...
at net.bull.javamelody.MonitoringFilter.doFilter(MonitoringFilter.java:232)
at net.bull.javamelody.MonitoringFilter.doFilter(MonitoringFilter.java:209)
at net.bull.javamelody.PluginMonitoringFilter.doFilter(PluginMonitoringFilter.java:88)
at net.bull.javamelody.LiferayMonitoringFilter.doFilter(LiferayMonitoringFilter.java:108)
...
Caused by: com.liferay.portal.kernel.exception.SystemException: java.lang.NullPointerException
at com.liferay.portal.service.persistence.impl.BasePersistenceImpl.processException(BasePersistenceImpl.java:251)
at com.liferay.counter.service.persistence.CounterFinderImpl._obtainIncrement(CounterFinderImpl.java:417)
at com.liferay.counter.service.persistence.CounterFinderImpl.createCounterRegister(CounterFinderImpl.java:255)
at com.liferay.counter.service.persistence.CounterFinderImpl.createCounterRegister(CounterFinderImpl.java:207)
at com.liferay.counter.service.persistence.CounterFinderImpl.getCounterRegister(CounterFinderImpl.java:282)
at com.liferay.counter.service.persistence.CounterFinderImpl.increment(CounterFinderImpl.java:118)
at com.liferay.counter.service.persistence.CounterFinderImpl.increment(CounterFinderImpl.java:109)
at com.liferay.counter.service.impl.CounterLocalServiceImpl.increment(CounterLocalServiceImpl.java:49)
sitecreation.log